Abstract 541: Evaluation of low-pass whole genome sequencing for the diagnosis and monitoring of patients with pediatric solid tumors
Authors: Eirini Christodoulou, Dejerianne Ostrow, Anya Zdanowicz, Venkata Yellapantula, Cameron O'Connell, Moiz Bootwalla, Pan Yachen, Jennifer Cotter, James Amatruda, Leo Mascarenhas, Fariba Navid, Gai Xiaowu, Jaclyn Biegel
Journal: Cancer Research (2022)

Abstract Liquid biopsy assays based on sequence analysis of cell-free circulating tumor DNA (cfDNA) have the potential to transform patient care. Recent advances, however, have primarily focused on adult patients with solid tumors from whom access to sufficient volumes of blood, urine or other bodily fluids is not a barrier to testing. For pediatric cancer patients, noninvasive procedures are of paramount importance for early diagnosis as well as effective monitoring of disease, but clinical diagnostic tests need to be optimized for low volumes of blood. Furthermore, most childhood solid tumors have a limited number of driver mutations that can be interrogated by targeted next generation sequencing (NGS) panels. We evaluated analysis of liquid biopsy using Low-Pass Whole Genome Sequencing (LP-WGS) of plasma cfDNA as a potential approach for diagnosing and monitoring pediatric solid tumors. We profiled samples from 42 patients with a variety of solid tumors including sarcoma (n = 28), germ-cell (n = 4), and renal tumors ( n = 10). cfDNA was extracted with the MagMax cell-free total nucleic acid extraction kit from 4-6ml peripheral blood collected in EDTA tubes at the time of diagnosis (if available), during and after chemotherapy, and when available, at relapse. Whole-genome sequencing libraries were constructed with the xGen Prism DNA Library Prep Kit using 5ng of cfDNA and paired-end sequenced on an Illumina NextSeq 500 at an average of 1x depth of coverage. Data was analyzed using iChor software. The LP-WGS data from the cfDNA samples was compared with copy number alteration (CNA) profiles of the primary tumors generated from clinical chromosomal microarray analysis (CMA) (CytoScanHD or OncoScan). The CNA profiles detected in plasma using LP-WGS were very similar to those of the primary tumors observed by CMA. Of 42 patients analyzed to date, 19 had non-informative profiles either at diagnosis or relapse. The loss of 9p and 17p, including CDKN2A and TP53 respectively, were the most common pathogenic CNAs detected in the abnormal cases. One patient’s germ cell tumor profiled with our OncoKids NGS panel had a confirmed KRAS mutation and 12p amplification that were also detected by LP-WGS in the liquid biopsy. Marked genomic instability characteristic of osteosarcoma was readily detectable by LP-WGS and an indication of response to therapy was mirrored by the absence of CNAs in the liquid biopsy specimen after treatment. Combined, these data suggest that liquid biopsy with LP-WGS may be used to monitor pediatric patients with solid tumors, from diagnosis through treatment and recurrence. Citation Format: Eirini Christodoulou, Dejerianne Ostrow, Anya Zdanowicz, Venkata Yellapantula, Cameron O'Connell, Moiz Bootwalla, Pan Yachen, Jennifer Cotter, James Amatruda, Leo Mascarenhas, Fariba Navid, Gai Xiaowu, Jaclyn Biegel. Evaluation of low-pass whole genome sequencing for the diagnosis and monitoring of patients with pediatric solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 541.